Epigenetic control of gene transcription, DNA synthesis and repair plays critical roles in the specification of cell fate and function, aging and carcinogenesis. Accessibility of the genome for these DNA-templated tasks depends on the distribution of nucleosomes, the fundamental repeating unit of chromatin composed of histone proteins and associated DNA. Nucleosome configuration is in turn regulated by a complex interplay among transcription factors, noncoding RNA, post-synthetic DNA and histone modifications, histone variants, and non-histone proteins that write, erase, and interpret chromatin-associated signals. Chromatin immunoprecipitation (ChIP) is the gold standard for probing protein-DNA interactions and is increasingly used in research aiming to identify molecular targets for individualized therapy (e.g., in cancer). In currently available ChIP assays, antibodies targeting specific chromatin components are used to purify fragmented DNA-protein complexes. The pendant DNA is then released and analyzed by qPCR or sequencing.
While powerful, traditional ChIP protocols require a large cellular input (106-107 cells), which limits their utility to study biopsies, rare cells (e.g., stem cells, circulating tumor cells), and to assess tumor heterogeneity. ChIP is also laborious, time-consuming, and highly influenced by user skills Recent advances in ChIP technologies including a handful of approaches utilize multi-layered, valved microfluidic devices, offer reduced sample sizes, increased parallelization, and the potential for automation. However, no single approach simultaneously offers these benefits. Furthermore, the published methods did not allow rigorous, genome-wide validation due to lack of scalability. Exemplary desirable improvements include a more comprehensive incorporation of the entire ChIP workflow, amenability to variable levels of cellular input, and on-chip processing that readily interfaces with downstream genomic analyses.